PeroxiBase: a database for large-scale evolutionary analysis of peroxidases

Abstract

The PeroxiBase (http://peroxibase.toulouse.inra.fr/) is a specialized database devoted to peroxidases’ families, which are major actors of stress responses. In addition to the increasing number of sequences and the complete modification of the Web interface, new analysis tools and functionalities have been developed since the previous publication in the NAR database issue. Nucleotide sequences and graphical representation of the gene structure can now be included for entries containing genomic cross-references. An expert semi-automatic annotation strategy is being developed to generate new entries from genomic sequences and from EST libraries. Plus, new internal and automatic controls have been included to improve the quality of the entries. To compare gene structure organization among families’ members, two new tools are available, CIWOG to detect common introns and GECA to visualize gene structure overlaid with sequence conservation. The multicriteria search tool was greatly improved to allow simple and combined queries. After such requests or a BLAST search, different analysis processes are suggested, such as multiple alignments with ClustalW or MAFFT, a platform for phylogenetic analysis and GECA’s display in association with a phylogenetic tree. Finally, we updated our family specific profiles implemented in the PeroxiScan tool and made new profiles to consider new sub-families.

Degradation of polycyclic aromatic hydrocarbons in soil by a tolerant strain of Trichoderma asperellum

“…Identified T. asperellum peroxidases include cytochrome C peroxidases, catalase peroxidases, glutathione peroxidise, and dye decolorizing (DyP-type) peroxidases (Fawal 2014). Although peroxidase activity in T. asperellum has been described mainly as a response against oxidative stress (Fawal et al 2013), VA-oxidizing peroxidase activity detected in strain H15 could in fact be related to DyP-type peroxidase (TaspDyPrx01, PeroxiBase ID 12842). DyP peroxidases possess a broad substrate specificity and have been previously described as LiP in Actinobacteria, having a significant role in bacterial lignin degradation (Ahmad et al 2011) as well as a role in fungal degradation of lignin by basidiomycetes (Liers et al 2011).…”

Characterization and application of a novel class II thermophilic peroxidase from Myceliophthora thermophila in biosynthesis of polycatechol

“…A PeroxiBase profile scan (PeroxiScan) identified the translated sequence as a general, non-animal peroxidase, belonging to Class II peroxidase superfamily, and more specifically at Ascomycetes Class II Type A peroxidases (http://peroxibase. toulouse.inra.fr/; [32]). …”

Bacterial and algal orthologs of prostaglandin H2 synthase: novel insights into the evolution of an integral membrane protein

“…Prostaglandin H 2 synthase homologs from crustaceans, coral, and alga PeroxiBase [71] curates a collection of peroxidase-related genes from all kingdoms of life, including 95 entries for open-reading frames (ORFs) which are predicted to possess structural homology to ovine PGHS based on primary sequence. In addition to mammalian ORFs, additional PGHS genes have been reported from a number of additional more primitive vertebrate [72] invertebrate, and plant species, including crustacean, coral, and algae [22,68,[73][74][75].…”